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Soft-rot Enterobacteriaceae (SRE), which belong to the genera Pectobacterium and Dickeya, consist mainly of broad host-range pathogens that cause wilt, rot, and blackleg diseases on a wide range of plants. They are found in plants, insects, soil, and water in agricultural regions worldwide. SRE encode all six known protein secretion systems present in gram-negative bacteria, and these systems are involved in attacking host plants and competing bacteria. They also produce and detect multiple types of small molecules to coordinate pathogenesis, modify the plant environment, attack competing microbes, and perhaps to attract insect vectors. This review integrates new information about the role protein secretion and detection and production of ions and small molecules play in soft-rot pathogenicity.

Phyllosphere microbial communities were evaluated on leaves of field-grown plant species by culture-dependent and -independent methods. Denaturing gradient gel electrophoresis (DGGE) with 16S rDNA primers generally indicated that microbial community structures were similar on different individuals of the same plant species, but unique on different plant species. Phyllosphere bacteria were identified from Citrus sinesis (cv. Valencia) by using DGGE analysis followed by cloning and sequencing of the dominant rDNA bands. Of the 17 unique sequences obtained, database queries showed only four strains that had been described previously as phyllosphere bacteria. Five of the 17 sequences had 16S similarities lower than 90% to database entries, suggesting that they represent previously undescribed species. In addition, three fungal species were also identified. Very different 16S rDNA DGGE banding profiles were obtained when replicate cv. Valencia leaf samples were cultured in BIOLOG EcoPlates for 4.5 days. All of these rDNA sequences had 97-100% similarity to those of known phyllosphere bacteria, but only two of them matched those identified by the culture independent DGGE analysis. Like other studied ecosystems, microbial phyllosphere communities therefore are more complex than previously thought, based on conventional culture-based methods.A ll plant species in natural habitats have associated epiphytic microflora comprising the so-called phyllosphere (1, 2). The composition and quantity of nutrients, including carbohydrates, organic acids, and amino acids that support the growth of epiphytic bacteria, are affected by the plant species, leaf age, leaf physiological status, and the presence of tissue damage (3). Similarly, host plants, leaf age, leaf position, physical environmental condition, and availability of immigrant inoculum have also been suggested to be involved in determining species of microbes in the phyllosphere (4-7).There has been much interest in life forms that inhabit extreme environments such as the phyllosphere. With the repeated, rapid alteration of environmental conditions occurring on leaf surfaces, the phyllosphere has been recognized as a hostile environment to bacteria (8). Leaf surfaces are often dry and temperatures can reach 40-55°C under intense sunlight. During the night, however, leaves are frequently wet with dew and at relatively cool temperatures (5-10°C). Strong UV radiation during the day and sparse nutritional (oligotrophic) conditions also contribute to stressful conditions in the phyllosphere (8). More than 85 different species of microorganisms in 37 genera have been reported in the phyllospheres of rye, olive, sugar beet, and wheat, all by culture-based methods (8-10). Most of these bacteria establish large populations with no apparent effect on the plant, but a few of them can infect the leaves and cause disease (1).Microbial ecologists have devoted much effort to investigating microbial diversity and studying biological interactions between species in the environment. Microor...

Root exudate composition and quantity vary in relation to plant nutritional status, but the impact of the differences on rhizosphere microbial communities is not known. To examine this question, we performed an experiment with barley (Hordeum vulgare) plants under iron-limiting and iron-sufficient growth conditions. Plants were grown in an iron-limiting soil in root box microcosms. One-half of the plants were treated with foliar iron every day to inhibit phytosiderophore production and to alter root exudate composition. After 30 days, the bacterial communities associated with different root zones, including the primary root tips, nonelongating secondary root tips, sites of lateral root emergence, and older roots distal from the tip, were characterized by using 16S ribosomal DNA (rDNA) fingerprints generated by PCR-denaturing gradient gel electrophoresis (DGGE). Our results showed that the microbial communities associated with the different root locations produced many common 16S rDNA bands but that the communities could be distinguished by using correspondence analysis. Approximately 40% of the variation between communities could be attributed to plant iron nutritional status. A sequence analysis of clones generated from a single 16S rDNA band obtained at all of the root locations revealed that there were taxonomically different species in the same band, suggesting that the resolving power of DGGE for characterization of community structure at the species level is limited. Our results suggest that the bacterial communities in the rhizosphere are substantially different in different root zones and that a rhizosphere community may be altered by changes in root exudate composition caused by changes in plant iron nutritional status.Root exudates selectively influence the growth of bacteria and fungi that colonize the rhizosphere by altering the chemistry of soil in the vicinity of the plant roots and by serving as selective growth substrates for soil microorganisms. Microorganisms in turn influence the composition and quantity of various root exudate components through their effects on root cell leakage, cell metabolism, and plant nutrition. Based on differences in root exudation and rhizodeposition in different root zones, rhizosphere microbial communities can vary in structure and species composition in different root locations or in relation to soil type, plant species, nutritional status, age, stress, disease, and other environmental factors (8,16,22,23). During the growth of new roots, exudates secreted in the zone of elongation behind the root tips support the growth of primary root colonizers that utilize easily degradable sugars and organic acids. In the older root zones, carbon is deposited primarily as sloughed cells and consists of more recalcitrant materials, including lignified cellulose and hemicellulose, so that fungi and bacteria in these zones are presumably adapted to crowded, oligotrophic conditions. Other nutritionally distinct sites include the sites of lateral root emergence and the secondary, ...

Agricultural soils are typically fumigated to provide effective control of nematodes, soilborne pathogens, and weeds in preparation for planting of high-value cash crops. The ability of soil microbial communities to recover after treatment with fumigants was examined using culture-dependent (Biolog) and culture-independent (phospholipid fatty acid [PLFA] analysis and denaturing gradient gel electrophoresis [DGGE] of 16S ribosomal DNA [rDNA] fragments amplified directly from soil DNA) approaches. Changes in soil microbial community structure were examined in a microcosm experiment following the application of methyl bromide (MeBr), methyl isothiocyanate, 1,3-dichloropropene (1,3-D), and chloropicrin. Variations among Biolog fingerprints showed that the effect of MeBr on heterotrophic microbial activities was most severe in the first week and that thereafter the effects of MeBr and the other fumigants were expressed at much lower levels. The results of PLFA analysis demonstrated a community shift in all treatments to a community dominated by gram-positive bacterial biomass. Different 16S rDNA profiles from fumigated soils were quantified by analyzing the DGGE band patterns. The Shannon-Weaver index of diversity, H, was calculated for each fumigated soil sample. High diversity indices were maintained between the control soil and the fumigant-treated soils, except for MeBr (H decreased from 1.14 to 0.13). After 12 weeks of incubation, H increased to 0.73 in the MeBr-treated samples. Sequence analysis of clones generated from unique bands showed the presence of taxonomically unique clones that had emerged from the MeBr-treated samples and were dominated by clones closely related to Bacillus spp. and Heliothrix oregonensis. Variations in the data were much higher in the Biolog assay than in the PLFA and DGGE assays, suggesting a high sensitivity of PLFA analysis and DGGE in monitoring the effects of fumigants on soil community composition and structure. Our results indicate that MeBr has the greatest impact on soil microbial communities and that 1,3-D has the least impact.